ArticleNucleic acids research2011
miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Syndecan-1 Controls Lung Tumorigenesis by Regulating miRNAs Packaged in Exosomes.The American journal of pathology · 2018Article
- Evidence for the role of microRNA 374b in acquired cisplatin resistance in pancreatic cancer cells.Cancer gene therapy · 2016Article
- RISC-mediated control of selected chromatin regulators stabilizes ground state pluripotency of mouse embryonic stem cells.Genome biology · 2016Article
- Article
- Integrated analysis of mRNA and miRNA expression in response to interleukin-6 in hepatocytes.Data in brief · 2015Article
- cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.Nucleic acids research · 2015Article
- Integrative analysis of multi-omics data for identifying multi-markers for diagnosing pancreatic cancer.BMC genomics · 2015Article
- A high-resolution network model for global gene regulation in Mycobacterium tuberculosis.Nucleic acids research · 2014Article
- Article
- A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen.Genome research · 2013Article
- Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions.Nucleic acids research · 2013Article
- Clinical advances in molecular biomarkers for cancer diagnosis and therapy.International journal of molecular sciences · 2013Review
- Time-dependent changes in gene expression induced by secreted amyloid precursor protein-alpha in the rat hippocampus.BMC genomics · 2013Article
- A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers.Genome research · 2012Article
- Reverse engineering systems models of regulation: discovery, prediction and mechanisms.Current opinion in biotechnology · 2012Review
- Inferring the regulatory network behind a gene expression experiment.Nucleic acids research · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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Abstract
Transcriptome profiling studies have produced staggering numbers of gene co-expression signatures for a variety of biological systems. A significant fraction of these signatures will be partially or fully explained by miRNA-mediated targeted transcript degradation. miRvestigator takes as input lists of co-expressed genes from Caenorhabditis elegans, Drosophila melanogaster, G. gallus, Homo sapiens, Mus musculus or Rattus norvegicus and identifies the specific miRNAs that are likely to bind to 3' un-translated region (UTR) sequences to mediate the observed co-regulation. The novelty of our approach is the miRvestigator hidden Markov model (HMM) algorithm which systematically computes a similarity P-value for each unique miRNA seed sequence from the miRNA database miRBase to an overrepresented sequence motif identified within the 3'-UTR of the query genes. We have made this miRNA discovery tool accessible to the community by integrating our HMM algorithm with a proven algorithm for de novo discovery of miRNA seed sequences and wrapping these algorithms into a user-friendly interface. Additionally, the miRvestigator web server also produces a list of putative miRNA binding sites within 3'-UTRs of the query transcripts to facilitate the design of validation experiments. The miRvestigator is freely available at http://mirvestigator.systemsbiology.net.
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Registered trials
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